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Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
Matentzoglu, Nicolas; Goutte-Gattat, Damien; Tan, Shawn Zheng Kai; Balhoff, James P; Carbon, Seth; Caron, Anita R; Duncan, William D; Flack, Joe E; Haendel, Melissa; Harris, Nomi L; Hogan, William R; Hoyt, Charles Tapley; Jackson, Rebecca C; Kim, HyeongSik; Kir, Huseyin; Larralde, Martin; McMurry, Julie A; Overton, James A; Peters, Bjoern; Pilgrim, Clare; Stefancsik, Ray; Robb, Sofia Mc; Toro, Sabrina; Vasilevsky, Nicole A; Walls, Ramona; Mungall, Christopher J; Osumi-Sutherland, David.
Afiliação
  • Matentzoglu N; Semanticly, Spaces Ermou Ermou 56, Athens 10563 ΓΕΜΗ 160976003000, Greece.
  • Goutte-Gattat D; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
  • Tan SZK; Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Balhoff JP; RENCI, University of North Carolina, Chapel Hill, NC, North Carolina 27517, USA.
  • Carbon S; Berkeley Bioinformatics Open-source Projects (BBOP), Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mailstop 977-0257, Berkeley, CA 94720, USA.
  • Caron AR; Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Duncan WD; Berkeley Bioinformatics Open-source Projects (BBOP), Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mailstop 977-0257, Berkeley, CA 94720, USA.
  • Flack JE; College of Dentistry; Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, William D. Duncan: 1395 Center Dr, Gainesville, William R. Hogan: 1600 SW Archer Rd, Gainesville, FL 32610, USA.
  • Haendel M; School of Medicine, Johns Hopkins University, 733 N Broadway, Baltimore, Baltimore, MD 21205, USA.
  • Harris NL; University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA.
  • Hogan WR; Berkeley Bioinformatics Open-source Projects (BBOP), Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mailstop 977-0257, Berkeley, CA 94720, USA.
  • Hoyt CT; College of Dentistry; Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, William D. Duncan: 1395 Center Dr, Gainesville, William R. Hogan: 1600 SW Archer Rd, Gainesville, FL 32610, USA.
  • Jackson RC; Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue Armenise Building Room 109, Boston, MA 02115, USA.
  • Kim H; Bend Informatics LLC, 5305 RIVER RD NORTH, STE B, KEIZER, OR 97303, USA.
  • Kir H; Robert Bosch LLC, Sunnyvale, CA 94085, USA.
  • Larralde M; Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • McMurry JA; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany.
  • Overton JA; University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA.
  • Peters B; Knocean Inc., Toronto, Ontario, ON M6P 2T3, Canada.
  • Pilgrim C; Institute for Allergy & Immunology, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
  • Stefancsik R; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK.
  • Robb SM; Samples Phenotypes and Ontologies Team (SPOT), European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
  • Toro S; Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA.
  • Vasilevsky NA; University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA.
  • Walls R; University of Colorado Anschutz Medical Campus, 13001 E 17th Pl, Aurora, CO 80045, USA.
  • Mungall CJ; Critical Path Institute, 1730 E River Road, Tucson, AZ 85718, USA.
  • Osumi-Sutherland D; Berkeley Bioinformatics Open-source Projects (BBOP), Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mailstop 977-0257, Berkeley, CA 94720, USA.
Database (Oxford) ; 20222022 10 08.
Article em En | MEDLINE | ID: mdl-36208225
ABSTRACT
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community. Database URL https//github.com/INCATools/ontology-development-kit.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Ontologias Biológicas Tipo de estudo: Guideline Idioma: En Revista: Database (Oxford) Ano de publicação: 2022 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Ontologias Biológicas Tipo de estudo: Guideline Idioma: En Revista: Database (Oxford) Ano de publicação: 2022 Tipo de documento: Article